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- PDB-8h63: Crystal structure of Internalin A from Listeria monocytogenes wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h63 | ||||||
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Title | Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound | ||||||
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![]() | CELL INVASION/IMMUNE SYSTEM / Internalin A Cadherin Bacterial invasion nanobody Surface plasmon resonance Isothermal titration calorimetry / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() InlA-mediated entry of Listeria monocytogenes into host cells / peptidoglycan-based cell wall / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caaveiro, J.M.M. / Nagatoish, S. / Tsumoto, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. Authors: Yamazaki, T. / Nagatoishi, S. / Yamawaki, T. / Nozawa, T. / Matsunaga, R. / Nakakido, M. / Caaveiro, J.M.M. / Nakagawa, I. / Tsumoto, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.1 KB | Display | ![]() |
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PDB format | ![]() | 110.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464 KB | Display | ![]() |
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Full document | ![]() | 465.9 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h62SC ![]() 8h64C ![]() 6jb9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Antibody , 2 types, 2 molecules AB
#1: Protein | Mass: 49914.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-679 / EGD-e / Gene: inlA, lmo0433,intlA / Production host: ![]() ![]() |
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#2: Antibody | Mass: 12732.190 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 770 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EPE / | ||||
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#4: Chemical | ChemComp-IPA / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.085 M HEPES sodium pH 7.0; 8.5% Isopropanol; 20% PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→33.3 Å / Num. obs: 91994 / % possible obs: 96.6 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.042 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.53→1.61 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12582 / CC1/2: 0.752 / Rpim(I) all: 0.294 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8H62 6JB9 Resolution: 1.53→31.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.412 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.15 Å2 / Biso mean: 15.245 Å2 / Biso min: 6.68 Å2
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Refinement step | Cycle: final / Resolution: 1.53→31.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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